Evaluating various composite sampling modes for detecting pathogenic SARS-CoV-2 virus in raw sewage

Li, Ye; Ash, Kurt T.; Joyner, Dominique C.; Williams, Daniel E.; Alamilla, Isabella; McKay, Peter J.; Iler, Chris; Hazen, Terry C.

doi:10.3389/fmicb.2023.1305967

Evaluating various composite sampling modes for detecting pathogenic SARS-CoV-2 virus in raw sewage

Journal Article · Thu Nov 23 00:00:00 EST 2023 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2023.1305967· OSTI ID:2283822

Li, Ye ^[1]; ^[2]; Joyner, Dominique C. ^[2]; Williams, Daniel E. ^[2]; Alamilla, Isabella ^[1]; McKay, Peter J. ^[1]; Iler, Chris ^[1]; ^[2]

Univ. of Tennessee, Knoxville, TN (United States)
Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Inadequate sampling approaches to wastewater analyses can introduce biases, leading to inaccurate results such as false negatives and significant over- or underestimation of average daily viral concentrations, due to the sporadic nature of viral input. To address this challenge, we conducted a field trial within the University of Tennessee residence halls, employing different composite sampling modes that encompassed different time intervals (1 h, 2 h, 4 h, 6 h, and 24 h) across various time windows (morning, afternoon, evening, and late-night). Our primary objective was to identify the optimal approach for generating representative composite samples of SARS-CoV-2 from raw wastewater. Utilizing reverse transcription-quantitative polymerase chain reaction, we quantified the levels of SARS-CoV-2 RNA and pepper mild mottle virus (PMMoV) RNA in raw sewage. Our findings consistently demonstrated that PMMoV RNA, an indicator virus of human fecal contamination in water environment, exhibited higher abundance and lower variability compared to pathogenic SARS-CoV-2 RNA. Significantly, both SARS-CoV-2 and PMMoV RNA exhibited greater variability in 1 h individual composite samples throughout the entire sampling period, contrasting with the stability observed in other time-based composite samples. Through a comprehensive analysis of various composite sampling modes using the Quade Nonparametric ANCOVA test with date, PMMoV concentration and site as covariates, we concluded that employing a composite sampler during a focused 6 h morning window for pathogenic SARS-CoV-2 RNA is a pragmatic and cost-effective strategy for achieving representative composite samples within a single day in wastewater-based epidemiology applications. This method has the potential to significantly enhance the accuracy and reliability of data collected at the community level, thereby contributing to more informed public health decision-making during a pandemic.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 2283822

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Journal Issue: 2023 Vol. 14; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

References (58)

Implementing wastewater surveillance for SARS‐CoV‐2 on a university campus: Lessons learned Wartell, Brian A.; Proano, Camila; Bakalian, Lena Water Environment Research, Vol. 94, Issue 11 https://doi.org/10.1002/wer.10807	journal	November 2022
Intraday variability of indicator and pathogenic viruses in 1-h and 24-h composite wastewater samples: Implications for wastewater-based epidemiology Ahmed, Warish; Bivins, Aaron; Bertsch, Paul M. Environmental Research, Vol. 193 https://doi.org/10.1016/j.envres.2020.110531	journal	February 2021
Targeted wastewater surveillance of SARS-CoV-2 on a university campus for COVID-19 outbreak detection and mitigation Scott, Laura C.; Aubee, Alexandra; Babahaji, Layla Environmental Research, Vol. 200 https://doi.org/10.1016/j.envres.2021.111374	journal	September 2021
Wastewater surveillance of SARS-CoV-2 in dormitories as a part of comprehensive university campus COVID-19 monitoring Lu, Emily; Ai, Yuehan; Davis, Angela Environmental Research, Vol. 212 https://doi.org/10.1016/j.envres.2022.113580	journal	September 2022
Building-level wastewater surveillance of SARS-CoV-2 is associated with transmission and variant trends in a university setting Sellers, Sarah C.; Gosnell, Emily; Bryant, Dillon Environmental Research, Vol. 215 https://doi.org/10.1016/j.envres.2022.114277	journal	December 2022
Metropolitan wastewater analysis for COVID-19 epidemiological surveillance Randazzo, Walter; Cuevas-Ferrando, Enric; Sanjuán, Rafael International Journal of Hygiene and Environmental Health, Vol. 230 https://doi.org/10.1016/j.ijheh.2020.113621	journal	September 2020
Wastewater surveillance of SARS-CoV-2 and chemical markers in campus dormitories in an evolving COVID − 19 pandemic Mohapatra, Sanjeeb; Bhatia, Sumedha; Senaratna, Kavindra Yohan Kuhatheva Journal of Hazardous Materials, Vol. 446 https://doi.org/10.1016/j.jhazmat.2022.130690	journal	March 2023
COVID-19 containment on a college campus via wastewater-based epidemiology, targeted clinical testing and an intervention Betancourt, Walter Q.; Schmitz, Bradley W.; Innes, Gabriel K. Science of The Total Environment, Vol. 779 https://doi.org/10.1016/j.scitotenv.2021.146408	journal	July 2021
Implementing building-level SARS-CoV-2 wastewater surveillance on a university campus Gibas, Cynthia; Lambirth, Kevin; Mittal, Neha Science of The Total Environment, Vol. 782 https://doi.org/10.1016/j.scitotenv.2021.146749	journal	August 2021
Lessons learned from SARS-CoV-2 measurements in wastewater Sharkey, Mark E.; Kumar, Naresh; Mantero, Alejandro M. A. Science of The Total Environment, Vol. 798 https://doi.org/10.1016/j.scitotenv.2021.149177	journal	December 2021
Enumerating asymptomatic COVID-19 cases and estimating SARS-CoV-2 fecal shedding rates via wastewater-based epidemiology Schmitz, Bradley W.; Innes, Gabriel K.; Prasek, Sarah M. Science of The Total Environment, Vol. 801 https://doi.org/10.1016/j.scitotenv.2021.149794	journal	December 2021
SARS-CoV-2 variant detection at a university dormitory using wastewater genomic tools Vo, Van; Tillett, Richard L.; Chang, Ching-Lan Science of The Total Environment, Vol. 805 https://doi.org/10.1016/j.scitotenv.2021.149930	journal	January 2022
SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases Wu, Fuqing; Xiao, Amy; Zhang, Jianbo Science of The Total Environment, Vol. 805 https://doi.org/10.1016/j.scitotenv.2021.150121	journal	January 2022
Building knowledge of university campus population dynamics to enhance near-to-source sewage surveillance for SARS-CoV-2 detection Sweetapple, Chris; Melville-Shreeve, Peter; Chen, Albert S. Science of The Total Environment, Vol. 806 https://doi.org/10.1016/j.scitotenv.2021.150406	journal	February 2022
Improving the quality of wastewater treatment plant monitoring by adopting proper sampling strategies and data processing criteria Bertanza, Giorgio; Boiocchi, Riccardo; Pedrazzani, Roberta Science of The Total Environment, Vol. 806 https://doi.org/10.1016/j.scitotenv.2021.150724	journal	February 2022
A sensitive, simple, and low-cost method for COVID-19 wastewater surveillance at an institutional level Liu, Pengbo; Ibaraki, Makoto; VanTassell, Jamie Science of The Total Environment, Vol. 807 https://doi.org/10.1016/j.scitotenv.2021.151047	journal	February 2022
Comparison of residential dormitory COVID-19 monitoring via weekly saliva testing and sewage monitoring Fahrenfeld, N. L.; Morales Medina, William R.; D'Elia, Stephanie Science of The Total Environment, Vol. 814 https://doi.org/10.1016/j.scitotenv.2021.151947	journal	March 2022
Comparison of high-frequency in-pipe SARS-CoV-2 wastewater-based surveillance to concurrent COVID-19 random clinical testing on a public U.S. university campus Wright, Jillian; Driver, Erin M.; Bowes, Devin A. Science of The Total Environment, Vol. 820 https://doi.org/10.1016/j.scitotenv.2021.152877	journal	May 2022
Early warning of a COVID-19 surge on a university campus based on wastewater surveillance for SARS-CoV-2 at residence halls Wang, Yuke; Liu, Pengbo; Zhang, Haisu Science of The Total Environment, Vol. 821 https://doi.org/10.1016/j.scitotenv.2022.153291	journal	May 2022
Coordination of SARS-CoV-2 wastewater and clinical testing of university students demonstrates the importance of sampling duration and collection time Anderson-Coughlin, Brienna L.; Shearer, Adrienne E. H.; Omar, Alexis N. Science of The Total Environment, Vol. 830 https://doi.org/10.1016/j.scitotenv.2022.154619	journal	July 2022
Predictive values of time-dense SARS-CoV-2 wastewater analysis in university campus buildings Welling, Claire M.; Singleton, David R.; Haase, Steven B. Science of The Total Environment, Vol. 835 https://doi.org/10.1016/j.scitotenv.2022.155401	journal	August 2022
Monitoring the evolution of SARS-CoV-2 on a Spanish university campus through wastewater analysis: A pilot project for the reopening strategy de Llanos, Rosa; Cejudo-Marín, Rocío; Barneo, Manuela Science of The Total Environment, Vol. 845 https://doi.org/10.1016/j.scitotenv.2022.157370	journal	November 2022
Sewage surveillance of SARS-CoV-2 at student campus residences in the Western Cape, South Africa Mangwana, Noluxabiso; Archer, Edward; Muller, Christo J. F. Science of The Total Environment, Vol. 851 https://doi.org/10.1016/j.scitotenv.2022.158028	journal	December 2022
Long-term passive wastewater surveillance of SARS-CoV-2 for seven university dormitories in comparison to municipal surveillance Jain, N.; Hamilton, D.; Mital, S. Science of The Total Environment, Vol. 852 https://doi.org/10.1016/j.scitotenv.2022.158421	journal	December 2022
Predicting COVID-19 cases using SARS-CoV-2 RNA in air, surface swab and wastewater samples Solo-Gabriele, Helena M.; Kumar, Shelja; Abelson, Samantha Science of The Total Environment, Vol. 857 https://doi.org/10.1016/j.scitotenv.2022.159188	journal	January 2023
Parallel deployment of passive and composite samplers for surveillance and variant profiling of SARS-CoV-2 in sewage Cha, Gyuhyon; Graham, Katherine E.; Zhu, Kevin J. Science of The Total Environment, Vol. 866 https://doi.org/10.1016/j.scitotenv.2022.161101	journal	March 2023
Co-incidence of BA.1 and BA.2 at the start of Singapore's Omicron wave revealed by Community and University Campus wastewater surveillance Chua, Feng Jun Desmond; Kim, Se Yeon; Hill, Eric Science of The Total Environment, Vol. 875 https://doi.org/10.1016/j.scitotenv.2023.162611	journal	June 2023
SARS-CoV-2 wastewater monitoring in rural and small metropolitan communities in Central Michigan Conway, Michael J.; Kado, Stephanie; Kooienga, Breanna K. Science of The Total Environment, Vol. 894 https://doi.org/10.1016/j.scitotenv.2023.165013	journal	October 2023
High-resolution within-sewer SARS-CoV-2 surveillance facilitates informed intervention Reeves, Katelyn; Liebig, Jennifer; Feula, Antonio Water Research, Vol. 204 https://doi.org/10.1016/j.watres.2021.117613	journal	October 2021
Campus node-based wastewater surveillance enables COVID-19 case localization and confirms lower SARS-CoV-2 burden relative to the surrounding community Lee, Jangwoo; Acosta, Nicole; Waddell, Barbara J. Water Research, Vol. 244 https://doi.org/10.1016/j.watres.2023.120469	journal	October 2023
Inferring SARS-CoV-2 RNA shedding into wastewater relative to the time of infection Cavany, Sean; Bivins, Aaron; Wu, Zhenyu Epidemiology and Infection, Vol. 150 https://doi.org/10.1017/S0950268821002752	journal	January 2022
Wastewater Surveillance during Mass COVID-19 Vaccination on a College Campus Bivins, Aaron; Bibby, Kyle Environmental Science & Technology Letters, Vol. 8, Issue 9 https://doi.org/10.1021/acs.estlett.1c00519	journal	August 2021
Comparative Analysis of RNA-Extraction Approaches and Associated Influences on RT-qPCR of the SARS-CoV-2 RNA in a University Residence Hall and Quarantine Location Langan, Laura M.; O’Brien, Megan; Rundell, Zach C. ACS ES&T Water, Vol. 2, Issue 11 https://doi.org/10.1021/acsestwater.1c00476	journal	April 2022
Development and Validation of a Simplified Method for Analysis of SARS-CoV-2 RNA in University Dormitories Strike, William; Amirsoleimani, Atena; Olaleye, Abisola ACS ES&T Water, Vol. 2, Issue 11 https://doi.org/10.1021/acsestwater.2c00044	journal	May 2022
Relationships between SARS-CoV-2 in Wastewater and COVID-19 Clinical Cases and Hospitalizations, with and without Normalization against Indicators of Human Waste Zhan, Qingyu; Babler, Kristina M.; Sharkey, Mark E. ACS ES&T Water, Vol. 2, Issue 11 https://doi.org/10.1021/acsestwater.2c00045	journal	May 2022
SARS-CoV-2 RNA and N Antigen Quantification via Wastewater at the Campus Level, Building Cluster Level, and Individual-Building Level Zambrana, Winnie; Catoe, David; Coffman, Mhara M. ACS ES&T Water, Vol. 2, Issue 11 https://doi.org/10.1021/acsestwater.2c00050	journal	May 2022
Building-Level Wastewater Surveillance for SARS-CoV-2 in Occupied University Dormitories as an Outbreak Forecasting Tool: One Year Case Study Kotay, Shireen M.; Tanabe, Kawai O.; Colosi, Lisa M. ACS ES&T Water, Vol. 2, Issue 11 https://doi.org/10.1021/acsestwater.2c00057	journal	June 2022
Wastewater Surveillance of SARS-CoV-2 at a Canadian University Campus and the Impact of Wastewater Characteristics on Viral RNA Detection Bitter, Lena Carolin; Kibbee, Richard; Jiménez, Gabriela C. ACS ES&T Water, Vol. 2, Issue 11 https://doi.org/10.1021/acsestwater.2c00060	journal	May 2022
Retrospective Analysis of Wastewater-Based Epidemiology of SARS-CoV-2 in Residences on a Large College Campus: Relationships between Wastewater Outcomes and COVID-19 Cases across Two Semesters with Different COVID-19 Mitigation Policies Rainey, Andrew L.; Buschang, Katherine; O’Connor, Amber ACS ES&T Water, Vol. 3, Issue 1 https://doi.org/10.1021/acsestwater.2c00275	journal	December 2022
Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission Karthikeyan, Smruthi; Levy, Joshua I.; De Hoff, Peter Nature, Vol. 609, Issue 7925 https://doi.org/10.1038/s41586-022-05049-6	journal	July 2022
Building-level wastewater surveillance using tampon swabs and RT-LAMP for rapid SARS-CoV-2 RNA detection Bivins, Aaron; Lott, Megan; Shaffer, Marlee Environmental Science: Water Research & Technology, Vol. 8, Issue 1 https://doi.org/10.1039/D1EW00496D	journal	January 2022
Effectiveness of building-level sewage surveillance during both community-spread and sporadic-infection phases of SARS-CoV-2 in a university campus population Johnson, William; Reeves, Katelyn; Liebig, Jennifer FEMS Microbes, Vol. 3 https://doi.org/10.1093/femsmc/xtac024	journal	September 2022
The Implementation and Utilization of Wastewater-Based Epidemiology: Experiences From a Local Health Department Swain, Michael J.; Carter, Bonnie; Snowdon, Kimberly Journal of Public Health Management and Practice, Vol. 29, Issue 3 https://doi.org/10.1097/phh.0000000000001714	journal	January 2023
Pepper Mild Mottle Virus as an Indicator of Fecal Pollution Rosario, Karyna; Symonds, Erin M.; Sinigalliano, Christopher Applied and Environmental Microbiology, Vol. 75, Issue 22 https://doi.org/10.1128/AEM.00410-09	journal	November 2009
Development of Wastewater Pooled Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Congregate Living Settings Colosi, Lisa M.; Barry, Katie E.; Kotay, Shireen M. Applied and Environmental Microbiology, Vol. 87, Issue 13 https://doi.org/10.1128/AEM.00433-21	journal	June 2021
SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases Wu, Fuqing; Zhang, Jianbo; Xiao, Amy mSystems, Vol. 5, Issue 4 https://doi.org/10.1128/msystems.00614-20	journal	July 2020
Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus Karthikeyan, Smruthi; Nguyen, Andrew; McDonald, Daniel mSystems, Vol. 6, Issue 4 https://doi.org/10.1128/msystems.00793-21	journal	August 2021
Building-Level Detection Threshold of SARS-CoV-2 in Wastewater Rondeau, Nicole C.; Rose, Oliver J.; Alt, Ellen R. Microbiology Spectrum, Vol. 11, Issue 2 https://doi.org/10.1128/spectrum.02929-22	journal	April 2023
Wastewater surveillance of SARS-CoV-2 mutational profiles at a university and its surrounding community reveals a 20G outbreak on campus Swift, Candice L.; Isanovic, Mirza; Correa Velez, Karlen E. PLOS ONE, Vol. 17, Issue 4 https://doi.org/10.1371/journal.pone.0266407	journal	April 2022
Wastewater surveillance in smaller college communities may aid future public health initiatives Lee, Laura; Valmond, Lescia; Thomas, John PLOS ONE, Vol. 17, Issue 9 https://doi.org/10.1371/journal.pone.0270385	journal	September 2022
One health genomic surveillance and response to a university-based outbreak of the SARS-CoV-2 Delta AY.25 lineage, Arizona, 2021 Yaglom, Hayley D.; Maurer, Matthew; Collins, Brooke PLOS ONE, Vol. 17, Issue 10 https://doi.org/10.1371/journal.pone.0272830	journal	October 2022
Detection of SARS-CoV-2 RNA in wastewater from an enclosed college campus serves as an early warning surveillance system Kazenelson, Jacob; Jefferson, Tori; Rhodes, Ryan G. PLOS ONE, Vol. 18, Issue 7 https://doi.org/10.1371/journal.pone.0288808	journal	July 2023
Whole campus wastewater surveillance of SARS-CoV-2 for COVID-19 outbreak management Sharaby, Y.; Gilboa, Y.; Alfiya, Y. Water Science and Technology, Vol. 87, Issue 4 https://doi.org/10.2166/wst.2023.030	journal	February 2023
SARS-CoV-2 raw wastewater surveillance from student residences on an urban university campus Ash, K. T.; Li, Y.; Alamilla, I. Frontiers in Microbiology, Vol. 14 https://doi.org/10.3389/fmicb.2023.1101205	journal	February 2023
Decay of enveloped SARS-CoV-2 and non-enveloped PMMoV RNA in raw sewage from university dormitories Li, Ye; Ash, K. T.; Joyner, Dominique C. Frontiers in Microbiology, Vol. 14 https://doi.org/10.3389/fmicb.2023.1144026	journal	April 2023
Actionable wastewater surveillance: application to a university residence hall during the transition between Delta and Omicron resurgences of COVID-19 Corchis-Scott, Ryland; Geng, Qiudi; Al Riahi, Abdul Monem Frontiers in Public Health, Vol. 11 https://doi.org/10.3389/fpubh.2023.1139423	journal	May 2023
Quantifying the Relationship between SARS-CoV-2 Wastewater Concentrations and Building-Level COVID-19 Prevalence at an Isolation Residence: A Passive Sampling Approach Acer, Patrick T.; Kelly, Lauren M.; Lover, Andrew A. International Journal of Environmental Research and Public Health, Vol. 19, Issue 18 https://doi.org/10.3390/ijerph191811245	journal	September 2022
Comparison of Auto Sampling and Passive Sampling Methods for SARS-CoV-2 Detection in Wastewater Wilson, Melissa; Qiu, Yuanyuan; Yu, Jiaao Pathogens, Vol. 11, Issue 3 https://doi.org/10.3390/pathogens11030359	journal	March 2022

Similar Records

Monitoring SARS-CoV-2 in wastewater [Slides]

Technical Report · Mon Jul 25 00:00:00 EDT 2022 · OSTI ID:1878019

Monitoring SARS-CoV-2 in wastewater

Technical Report · Fri Aug 12 00:00:00 EDT 2022 · OSTI ID:1881788

Decay of enveloped SARS-CoV-2 and non-enveloped PMMoV RNA in raw sewage from university dormitories

Journal Article · Wed Apr 26 20:00:00 EDT 2023 · Frontiers in Microbiology · OSTI ID:1984337

Related Subjects

sampling timing
59 BASIC BIOLOGICAL SCIENCES
PMMoV RNA
SARS-CoV-2 RNA
raw sewage
sampling duration
sampling modes

Evaluating various composite sampling modes for detecting pathogenic SARS-CoV-2 virus in raw sewage

Citation Formats

References (58)

Similar Records

Related Subjects